| Previous changeset 2:565c0e690238 (2013-11-18) Next changeset 4:e423536a0780 (2014-04-10) |
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Commit message:
Uploaded |
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modified:
README tools/annovar/annovar.sh tools/annovar/annovar.xml |
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removed:
README~ tool_data_table_conf.xml.sample~ tool_dependencies.xml~ |
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| diff -r 565c0e690238 -r ff5325029a8e README --- a/README Mon Nov 18 10:32:33 2013 -0500 +++ b/README Thu Apr 10 09:15:32 2014 -0400 |
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| @@ -214,6 +214,9 @@ hg19_snp137.txt hg19_snp137NonFlagged.txt hg19_snp137NonFlagged.txt.idx +hg19_snp138.txt +hg19_snp138NonFlagged.txt +hg19_snp138NonFlagged.txt.idx hg19_tfbsConsSites.txt |
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| diff -r 565c0e690238 -r ff5325029a8e README~ --- a/README~ Mon Nov 18 10:32:33 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,213 +0,0 @@ -ANNOVAR needs to be installed manually in the following way: - - -1) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of - the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files) -1b) Restart galaxy instance for changes in .loc file to take effect - - -2) If you do not have ANNOVAR installed, request annovar download and sign license here: - http://www.openbioinformatics.org/annovar/annovar_download_form.php - - 3) Once downloaded, install annovar per the installation instructions and edit annovar.loc file to reflect location of directory containing perl scripts. - tool uses annotate_variation.pl and convert2annovar.pl - - 4) Then download all desired databases for all desired builds as follows: - annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb> - - where <humandb> is location where all database files should be stored - and <database> is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool) - and <build> can be hg18 or hg19 for humans, also other organisms available. - - list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html - - 5) edit the tool-data/annovar.loc file to reflect location of humandb folder - 5b) restart galaxy instance for changes in .loc file to take effect - -6) Tool uses cgatools join for combining of files, this should be installed automatically with repository. If not, get a copy from Complete Genomics directly: - wget http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz - tar xvzf cgatools-1.7.1.5-linux_binary-x86_64.tar.gz - - and place the "cgatools" binary found in bin/ directory on your $PATH - - -list of files in my own humandb folder: - - hg18_ALL.sites.2012_04.txt - hg18_ALL.sites.2012_04.txt.idx - hg18_avsift.txt - hg18_avsift.txt.idx - hg18_CEU.sites.2010_07.txt - hg18_CEU.sites.2010_07.txt.idx - hg18_cg46.txt - hg18_cg46.txt.idx - hg18_cg69.txt - hg18_cg69.txt.idx - hg18_cytoBand.txt - hg18_dgv.txt - hg18_ensGeneMrna.fa - hg18_ensGene.txt - hg18_esp5400_aa.txt - hg18_esp5400_aa.txt.idx - hg18_esp5400_all.txt - hg18_esp5400_all.txt.idx - hg18_esp5400_ea.txt - hg18_esp5400_ea.txt.idx - hg18_esp6500_aa.txt - hg18_esp6500_aa.txt.idx - hg18_esp6500_all.txt - hg18_esp6500_all.txt.idx - hg18_esp6500_ea.txt - hg18_esp6500_ea.txt.idx - hg18_esp6500si_aa.txt - hg18_esp6500si_aa.txt.idx - hg18_esp6500si_all.txt - hg18_esp6500si_all.txt.idx - hg18_esp6500si_ea.txt - hg18_esp6500si_ea.txt.idx - hg18_example_db_generic.txt - hg18_example_db_gff3.txt - hg18_genomicSuperDups.txt - hg18_gerp++gt2.txt - hg18_gerp++gt2.txt.idx - hg18_gwasCatalog.txt - hg18_JPTCHB.sites.2010_07.txt - hg18_JPTCHB.sites.2010_07.txt.idx - hg18_keggMapDesc.txt - hg18_keggPathway.txt - hg18_kgXref.txt - hg18_knownGeneMrna.fa - hg18_knownGene.txt - hg18_ljb_all.txt - hg18_ljb_all.txt.idx - hg18_ljb_lrt.txt - hg18_ljb_lrt.txt.idx - hg18_ljb_mt.txt - hg18_ljb_mt.txt.idx - hg18_ljb_phylop.txt - hg18_ljb_phylop.txt.idx - hg18_ljb_pp2.txt - hg18_ljb_pp2.txt.idx - hg18_ljb_sift.txt - hg18_ljb_sift.txt.idx - hg18_phastConsElements44way.txt - hg18_refGeneMrna.fa - hg18_refGene.txt - hg18_refLink.txt - hg18_snp128NonFlagged.txt - hg18_snp128NonFlagged.txt.idx - hg18_snp128.txt - hg18_snp128.txt.idx - hg18_snp129NonFlagged.txt - hg18_snp129NonFlagged.txt.idx - hg18_snp129.txt - hg18_snp129.txt.idx - hg18_snp130NonFlagged.txt - hg18_snp130NonFlagged.txt.idx - hg18_snp130.txt - hg18_snp130.txt.idx - hg18_snp131NonFlagged.txt - hg18_snp131NonFlagged.txt.idx - hg18_snp131.txt - hg18_snp131.txt.idx - hg18_snp132NonFlagged.txt - hg18_snp132NonFlagged.txt.idx - hg18_snp132.txt - hg18_snp132.txt.idx - hg18_tfbsConsSites.txt - hg18_YRI.sites.2010_07.txt - hg18_YRI.sites.2010_07.txt.idx - hg19_AFR.sites.2012_04.txt - hg19_AFR.sites.2012_04.txt.idx - hg19_ALL.sites.2010_11.txt - hg19_ALL.sites.2010_11.txt.idx - hg19_ALL.sites.2012_02.txt - hg19_ALL.sites.2012_02.txt.idx - hg19_ALL.sites.2012_04.txt - hg19_ALL.sites.2012_04.txt.idx - hg19_AMR.sites.2012_04.txt - hg19_AMR.sites.2012_04.txt.idx - hg19_ASN.sites.2012_04.txt - hg19_ASN.sites.2012_04.txt.idx - hg19_avsift.txt - hg19_avsift.txt.idx - hg19_cg46.txt - hg19_cg46.txt.idx - hg19_cg69.txt - hg19_cg69.txt.idx - hg19_cosmic61.txt - hg19_cosmic61.txt.idx - hg19_cosmic63.txt - hg19_cosmic63.txt.idx - hg19_cosmic64.txt - hg19_cosmic64.txt.idx - hg19_cosmic65.txt - hg19_cosmic65.txt.idx - hg19_cytoBand.txt - hg19_dgv.txt - hg19_ensGeneMrna.fa - hg19_ensGene.txt - hg19_esp5400_aa.txt - hg19_esp5400_aa.txt.idx - hg19_esp5400_all.txt - hg19_esp5400_all.txt.idx - hg19_esp5400_ea.txt - hg19_esp5400_ea.txt.idx - hg19_esp6500_aa.txt - hg19_esp6500_aa.txt.idx - hg19_esp6500_all.txt - hg19_esp6500_all.txt.idx - hg19_esp6500_ea.txt - hg19_esp6500_ea.txt.idx - hg19_esp6500si_aa.txt - hg19_esp6500si_aa.txt.idx - hg19_esp6500si_all.txt - hg19_esp6500si_all.txt.idx - hg19_esp6500si_ea.txt - hg19_esp6500si_ea.txt.idx - hg19_EUR.sites.2012_04.txt - hg19_EUR.sites.2012_04.txt.idx - hg19_genomicSuperDups.txt - hg19_gerp++gt2.txt - hg19_gerp++gt2.txt.idx - hg19_gwasCatalog.txt - hg19_keggMapDesc.txt - hg19_keggPathway.txt - hg19_kgXref.txt - hg19_knownGeneMrna.fa - hg19_knownGene.txt - hg19_ljb_all.txt - hg19_ljb_all.txt.idx - hg19_ljb_lrt.txt - hg19_ljb_lrt.txt.idx - hg19_ljb_mt.txt - hg19_ljb_mt.txt.idx - hg19_ljb_phylop.txt - hg19_ljb_phylop.txt.idx - hg19_ljb_pp2.txt - hg19_ljb_pp2.txt.idx - hg19_ljb_sift.txt - hg19_ljb_sift.txt.idx - hg19_phastConsElements46way.txt - hg19_refGeneMrna.fa - hg19_refGene.txt - hg19_refLink.txt - hg19_snp130NonFlagged.txt - hg19_snp130NonFlagged.txt.idx - hg19_snp130.txt - hg19_snp130.txt.idx - hg19_snp131NonFlagged.txt - hg19_snp131NonFlagged.txt.idx - hg19_snp131.txt - hg19_snp132NonFlagged.txt - hg19_snp132NonFlagged.txt.idx - hg19_snp132.txt - hg19_snp132.txt.idx - hg19_snp135NonFlagged.txt - hg19_snp135NonFlagged.txt.idx - hg19_snp135.txt - hg19_snp137NonFlagged.txt - hg19_snp137NonFlagged.txt.idx - hg19_snp137.txt - hg19_tfbsConsSites.txt - |
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| diff -r 565c0e690238 -r ff5325029a8e tool_data_table_conf.xml.sample~ --- a/tool_data_table_conf.xml.sample~ Mon Nov 18 10:32:33 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -<!-- ANNOVAR files --> -<table name="annovar_loc" comment_char="#"> -<columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns> -<file path="tool-data/annovar.loc" /> -</table> |
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| diff -r 565c0e690238 -r ff5325029a8e tool_dependencies.xml~ --- a/tool_dependencies.xml~ Mon Nov 18 10:32:33 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="cgatools17" version="1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action> - <action type="shell_command"> chmod a+x bin/cgatools</action> - <action type="move_file"> - <source>bin/cgatools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - Downloads and installs the cgatools binary. - </readme> - </package> -</tool_dependency> - |
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| diff -r 565c0e690238 -r ff5325029a8e tools/annovar/annovar.sh --- a/tools/annovar/annovar.sh Mon Nov 18 10:32:33 2013 -0500 +++ b/tools/annovar/annovar.sh Thu Apr 10 09:15:32 2014 -0400 |
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| @@ -179,7 +179,7 @@ ################################# -set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage +set -- `getopt -n$0 -u -a --longoptions="inputfile: buildver: humandb: varfile: VCF: chrcol: startcol: endcol: refcol: obscol: vartypecol: convertcoords: geneanno: hgvs: verdbsnp: tfbs: mce: cytoband: segdup: dgv: gwas: ver1000g: cg46: cg69: impactscores: newimpactscores: otherinfo: esp: gerp: cosmic61: cosmic63: cosmic64: cosmic65: cosmic67: cosmic68: clinvar: nci60: outall: outfilt: outinvalid: scriptsdir: dorunannovar: dofilter: filt_dbsnp: filt1000GALL: filt1000GAFR: filt1000GAMR: filt1000GASN: filt1000GEUR: filtESP6500ALL: filtESP6500EA: filtESP6500AA: filtcg46: filtcg69: dummy:" "h:" "$@"` || usage [ $# -eq 0 ] && usage @@ -201,7 +201,7 @@ --convertcoords) convertcoords=$2;shift;; # Y or N convert coordinate from CG to 1-based? --geneanno) geneanno=$2;shift;; # comma-separated list of strings refSeq, knowngene, ensgene --hgvs) hgvs=$2;shift;; - --verdbsnp) verdbsnp=$2;shift;; #comma-separated list of dbsnp version to annotate with (e.g. "132,135NonFlagged,137")" + --verdbsnp) verdbsnp=$2;shift;; #comma-separated list of dbsnp version to annotate with (e.g. "132,135NonFlagged,137,138")" --tfbs) tfbs=$2;shift;; # Y or N --mce) mce=$2;shift;; # Y or N --cytoband) cytoband=$2;shift;; # Y or N @@ -222,6 +222,7 @@ --cosmic64) cosmic64=$2;shift;; # Y or N --cosmic65) cosmic65=$2;shift;; # Y or N --cosmic67) cosmic67=$2;shift;; # Y or N + --cosmic68) cosmic68=$2;shift;; # Y or N --nci60) nci60=$2;shift;; # Y or N --clinvar) clinvar=$2;shift;; # Y or N --filt_dbsnp) filt_dbsnp=$2;shift;; @@ -483,7 +484,7 @@ if [ $vcf == "Y" ] #if CG varfile, convert then # convert vcf to annovarinput - $scriptsdir/convert2annovar.pl --format vcf4 --includeinfo --outfile annovarinput $infile 2>&1 + $scriptsdir/convert2annovar.pl --format vcf4old --allallele --includeinfo --outfile annovarinput $infile 2>&1 #construct header line from vcf file cat $infile | grep "#CHROM" > additionalcols @@ -1259,12 +1260,24 @@ fi + if [[ $cosmic68 == "Y" && $buildver == "hg19" ]] + then + echo -e "\nCOSMIC68 Annotation" + $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype cosmic68 annovarinput $humandb 2>&1 + + annovarout="annovarinput.${buildver}_cosmic68_dropped" + sed -i '1i\db\tCOSMIC68\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout + joinresults originalfile $annovarout 3 4 5 6 7 B.COSMIC68 + + fi + + if [[ $clinvar == "Y" && $buildver == "hg19" ]] then echo -e "\nCLINVAR Annotation" - $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype clinvar_20131105 annovarinput $humandb 2>&1 + $scriptsdir/annotate_variation.pl --filter --buildver $buildver -dbtype clinvar_20140211 annovarinput $humandb 2>&1 - annovarout="annovarinput.${buildver}_clinvar_20131105_dropped" + annovarout="annovarinput.${buildver}_clinvar_20140211_dropped" sed -i '1i\db\tCLINVAR\tchromosome\tstart\tend\treference\talleleSeq"'"$vcfheader"'"' $annovarout joinresults originalfile $annovarout 3 4 5 6 7 B.CLINVAR |
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| diff -r 565c0e690238 -r ff5325029a8e tools/annovar/annovar.xml --- a/tools/annovar/annovar.xml Mon Nov 18 10:32:33 2013 -0500 +++ b/tools/annovar/annovar.xml Thu Apr 10 09:15:32 2014 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="Annovar" name="ANNOVAR" version="2013aug"> +<tool id="AnnovarShed" name="ANNOVAR" version="2013aug"> <description> Annotate a file using ANNOVAR </description> <requirements> @@ -13,7 +13,8 @@ --cosmic63 ${cosmic63} --cosmic64 ${cosmic64} --cosmic65 ${cosmic65} - --cosmic67 ${cosmic67} + --cosmic67 ${cosmic67} + --cosmic68 ${cosmic68} --outall ${annotated} --outinvalid ${invalid} --dorunannovar ${dorun} @@ -130,7 +131,9 @@ <option value="snp135" > 135 (hg19 only) </option> <option value="snp135NonFlagged"> 135 NonFlagged </option> <option value="snp137" > 137 (hg19 only) </option> - <option value="snp137NonFlagged"> 137 NonFlagged </option> + <option value="snp137NonFlagged"> 137 NonFlagged </option> + <option value="snp138" > 138 (hg19 only) </option> + <option value="snp138NonFlagged"> 138 NonFlagged </option> </param> <param name="ver1000g" type="select" label="Select 1000Genomes Annotation(s)" multiple="true" display="checkboxes" optional="true" help="2012april database for ALL populations was converted to hg18 using the UCSC liftover program"> @@ -159,7 +162,7 @@ <param name="gerp" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="GERP++ Annotation?" help="GERP identifies constrained elements in multiple alignments by quantifying substitution deficits (see http://mendel.stanford.edu/SidowLab/downloads/gerp/ for details) This option annotates those variants having GERP++>2 in human genome, as this threshold is typically regarded as evolutionarily conserved and potentially functional"/> - <param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2013-11-05. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/> + <param name="clinvar" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="CLINVAR Annotation? (hg19 only)" help="version 2014-02-11. Annotations include Variant Clinical Significance (unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other) and Variant disease name."/> <param name="nci60" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with NCI60? (hg19 only)" help="NCI-60 exome allele frequency data"/> <param name="cgfortysix" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 46 Genomes?" help="Diversity Panel; 46 unrelated individuals"/> <param name="cgsixtynine" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Complete Genomics 69 Genomes?" help="Diversity Panel, Pedigree, YRI trio and PUR trio"/> @@ -168,6 +171,8 @@ <param name="cosmic64" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC64? (hg19 only)"/> <param name="cosmic65" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC65? (hg19 only)"/> <param name="cosmic67" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC67? (hg19 only)"/> + <param name="cosmic68" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="Annotate with COSMIC68? (hg19 only)"/> + <param name="newimpactscores" type="select" label="Select functional impact scores (LJB2)" multiple="true" display="checkboxes" optional="true" help="LJB refers to Liu, Jian, Boerwinkle paper in Human Mutation, pubmed ID 21520341. "> <option value="ljb2_sift"> SIFT score </option> |